August 31, 2013

This seems to parallel quite well with my hypothesis of a secondary expansion into Europe of the component I've labeled "West Asian", after the early Neolithic. From the paper:

The wild progenitor of barley, Hordeum spontaneum, is typically a winter-germinating species, responsive to day length (Turner et al. 2005), but recent work (H. Jones et al. 2008) has demonstrated that the non-responsive allele also occurs in wild barley in Israel, Jordan and Iran, in regions where this allele is favoured by the climatic conditions. There is strong evidence to suggest that the non-responsive allele in European cultivars (Group A) is genetically more similar to the allele in Iranian wild barleys than to the allele in wild barleys from Israel and Jordan.

and:

Detailed genetic comparisons between groups A, B and C (H. Jones 2008; H. Jones et al. 2008) suggest that Group A represents a more recent introduction of day-length non-responsive barley into Europe, rather than the selection of non-responsiveness from within populations that diffused into Europe in the Early Neolithic. In addition, three of the nine principal groups identified on the basis of the neutral SSR markers (groups 1–3) are genetically closely related and very similar in their phenotypic characteristics. They are located in north-west and Central Europe (Figure 3b), and are made up almost entirely of day-length non-responsive barleys (98 per cent) with a spring growth habit (98 per cent) (H. Jones et al. 2011). The distinctiveness of the landraces making up groups 1–3 suggests that the responsive/non-responsive difference between Southern and Northern Europe is not simply a reflection of current selective pressure but rather is one aspect of a more fundamental genetic difference between barley populations. These day-length non-responsive cultivars have therefore been interpreted as representing a later spread of barley into Northern Europe from the eastern part of the Fertile Crescent or beyond. This raises the issue of when they spread into Europe and whether or not they were introduced via the same route as the initial spread of agriculture.

and:

A possible channel for the introduction of day-length non-responsive barley into Northern Europe from the east at this time could have been through early exchange networks with metal-working communities of south-eastern Europe (Sherratt 1976; Bogucki 1999: 220–21). The Chalcolithic societies of the Balkans also maintained connections further east with the west Eurasian Steppes, Anatolia, and the Caucasus in the fifth and early fourth millennia, and copper was exchanged from west to east across the steppes north of the Black Sea (Kohl 2007: 31–39). Day-length non-responsive barley could, therefore, have travelled from east to west along the same route, north of the Black Sea via the Caucasus or, perhaps more likely given its agricultural nature, south of the Black Sea through Anatolia, possibly via a coastal route around the Black Sea, and then from the Carpatho-Balkan metallurgical region into Northern Europe (Figure 3b). A similar suggestion has been made for the later appearance of the oil plant Lallemantia, which was apparently introduced into Europe in the third millennium BC, possibly along the same trade routes as tin-bronzes (Valamoti & Jones 2010).

Antiquity Volume: 87 Number: 337 Page: 701–713

DNA evidence for multiple introductions of barley into Europe following dispersed domestications in Western Asia

G. Jones et al.

It has long been recognised that the Neolithic spread across Europe via two separate routes, one along the Mediterranean coasts, the other following the axis of the major rivers. But did these two streams have a common point of origin in south-west Asia, at least with regard to the principal plant and animals species that were involved? This study of barley DNA shows that the domesticated barley grown in Neolithic Europe falls into three separate types (groups A, B and C), each of which may have had a separate centre of origin in south-west Asia. Barley was relatively rarely cultivated by the early Linearbandkeramik farmers of Central and Northern Europe, but became more common during the fifth and fourth millennia BC. The analysis reported here indicates that a genetic variety of barley more suitable for northern growing conditions was introduced from south-west Asia at this period. It also suggests that the barley grown in south-eastern Europe at the very beginning of the Neolithic may have arrived there by different routes from two separate centres of domestication in south-west Asia. The multiple domestications that this pattern reveals imply that domestication may have been more a co-evolutionary process between plants and people than an intentional human action.

August 29, 2013

I haven't read this, but the idea of looking at looking at nuclear sequences of mitochondrial origin (numt) as a way of testing for archaic admixture seems interesting to me. Human mtDNA has a relatively shallow coalescence (less than 200 thousand years), with Neandertal mtDNA being a clear outgroup, and Denisovan mtDNA being an even more remote outgroup. If modern humans admixed with archaic ones (having mtDNA lineages much more remote than "Eve"), then the evidence may have been lost (due to drift) in mtDNA, but may have been preserved in the autosomes.

Africa demonstrates a complex process of the hominin evolution with a series of adaptive radiations during several millions of years that led to diverse morphological forms. Recently, Hammer et al. (2011) and Harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in Africa as recently as 35,000 years ago. However, a genetic evidence of hybridization between hominin lineages during the Lower and Middle Pleistocene epochs is unknown and the direct retrieval of DNA from extinct lineages of African hominins remains elusive. The availability of both nuclear and mitochondrial genome sequences from modern humans, Neanderthals, and Denisovans allows collecting nuclear DNA sequences of mitochondrial origin (numts) inserted into the nuclear genome of the ancestral hominin lineages and drawing conclusions about the hominin evolution in the remote past. The mtDNA and numt analysis uncovered a deep division of mtDNA lineages that existed in African hominins in the Middle Pleistocene. The first cluster included the human and Neanderthal-like mtDNA sequences while the second consisted of DNA sequences that are known today as mtAncestor-1, a nuclear fossil of the mtDNA, and the Denisova mtDNA isolated from a bone and a tooth found in southern Siberia. The two groups initially diverged 610,000-1,110,000 years ago. Approximately 220,000 years after the primary split, the Denisova - mtAncestor-1 mtDNA lineages mixed with the mtDNA pool of an ancestral population of Neanderthals and modern humans. This admixture after the profound division is demonstrated by the transposition of the Denisova-like mtDNA sequence into the nuclear genome of an ancestor of Neanderthals and modern humans. This finding suggests the matrilineal genetic structure among the Middle Pleistocene hominins as well as the existence of gene flow between African hominin lineages. Through paleogenomic analyses, it is impossible to exclude the theory that population structure and gene flow in African hominins influenced the admixture pattern observed in the nuclear genomes of non-Africans.

Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe

Ben Krause-Kyora et al.

Mesolithic populations throughout Europe used diverse resource exploitation strategies that focused heavily on collecting and hunting wild prey. Between 5500 and 4200 cal BC, agriculturalists migrated into northwestern Europe bringing a suite of Neolithic technologies including domesticated animals. Here we investigate to what extent Mesolithic Ertebølle communities in northern Germany had access to domestic pigs, possibly through contact with neighbouring Neolithic agricultural groups. We employ a multidisciplinary approach, applying sequencing of ancient mitochondrial and nuclear DNA (coat colour-coding gene MC1R) as well as traditional and geometric morphometric (molar size and shape) analyses in Sus specimens from 17 Neolithic and Ertebølle sites. Our data from 63 ancient pig specimens show that Ertebølle hunter-gatherers acquired domestic pigs of varying size and coat colour that had both Near Eastern and European mitochondrial DNA ancestry. Our results also reveal that domestic pigs were present in the region ~500 years earlier than previously demonstrated.

Population Growth Inflates the Per-Individual Number of Deleterious Mutations and Reduces Their Mean Effect

Elodie Gazave et al.

This study addresses the question of how purifying selection operates during recent rapid population growth such as has been experienced by human populations. This is not a straightforward problem because the human population is not at equilibrium: population genetics predicts that, on the one hand, the efficacy of natural selection increases as population size increases, eliminating ever more weakly deleterious variants; on the other hand, a larger number of deleterious mutations will be introduced into the population and will be more likely to increase in their number of copies as the population grows. To understand how patterns of human genetic variation have been shaped by the interaction of natural selection and population growth, we examined the trajectories of mutations with varying selection coefficients using computer simulations. We observed that while population growth dramatically increases the number of deleterious segregating sites in the population, it only mildly increases the number carried by each individual. Our simulations also show an increased efficacy of natural selection, reflected in a higher fraction of deleterious mutations eliminated at each generation, and a more efficient elimination of the most deleterious ones. As a consequence, while each individual carries a larger number of deleterious alleles than expected in the absence of growth, the average selection coefficient of each segregating allele is less deleterious. Combined, our results suggest that the genetic risk of complex diseases might be distributed across a larger number of more weakly deleterious rare variants.

The place of Armenian in the Indo-European language family: the relationship with Greek and Indo-Iranian*

Hrach Martirosyan

The main purpose of this paper is to present lexical correspondences that unite Armenian
with Greek and/or Indo-Iranian. They include shared innovations on the one hand, and isolated lexemes on the other. These two lexical corpora — lexical innovations on an inherited
basis and isolated words — can be placed within the same temporal and spatial framework.
After the Indo-European dispersal Proto-Armenian would have continued to come into
contact with genetically related Indo-European dialects. Simultaneously, it would certainly
also have been in contact with neighbouring non-Indo-European languages. A word can be
of a substrate origin if it is characterized by: (1) limited geographical distribution; (2) unusual phonology and word formation; (3) characteristic semantics. The material presented
here, albeit not exhaustive, allows to preliminarily conclude that Armenian, Greek, (Phrygian)
and Indo-Iranian were dialectally close to each other. Within this hypothetical dialect group,
Proto-Armenian was situated between Proto-Greek (to the west) and Proto-Indo-Iranian
(to the east). The Indo-Iranians then moved eastwards, while the Proto-Armenians and
Proto-Greeks remained in a common geographical region for a long period and developed
numerous shared innovations. At a later stage, together or independently, they borrowed a
large number of words from the Mediterranean / Pontic substrate language(s), mostly cultural and agricultural words, as well as animal and plant designations. On the other hand,
Armenian shows a considerable number of lexical correspondences with European branches
of the Indo-European language family, a large portion of which too should be explained in
terms of substrate rather than Indo-European heritage.

August 22, 2013

The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q

Vincenza Battaglia et al.

Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.

August 21, 2013

We report on the earliest archaeological evidence from the Faroe Islands, placing human colonization in the 4th–6th centuries AD, at least 300–500 years earlier than previously demonstrated archaeologically. The evidence consists of an extensive wind-blown sand deposit containing patches of burnt peat ash of anthropogenic origin. Samples of carbonised barley grains from two of these ash patches produced 14C dates of two pre-Viking phases within the 4th–6th and late 6th–8th centuries AD. A re-evaluation is required of the nature, scale and timing of the human colonization of the Faroes and the wider North Atlantic region.

August 16, 2013

Small carved stones unearthed in a nearly 5,000-year-old burial could represent the earliest gaming tokens ever found, according to Turkish archaeologists who are excavating early Bronze Age graves.

Found in a burial at Basur Höyük, a 820- by 492-foot mound near Siirt in southeast Turkey, the elaborate pieces consist of 49 small stones sculpted in different shapes and painted in green, red, blue, black and white.

"Some depict pigs, dogs and pyramids, others feature round and bullet shapes. We also found dice as well as three circular tokens made of white shell and topped with a black round stone," Haluk Saglamtimur of Ege University in Izmir, Turkey, told Discovery News.

This is a nice illustration of people's familiarity with several abstract geometrical shapes for the purposes of gaming.

August 15, 2013

The Late Bronze Age world of the Eastern Mediterranean, a rich linkage of Aegean, Egyptian, Syro-Palestinian, and Hittite civilizations, collapsed famously 3200 years ago and has remained one of the mysteries of the ancient world since the event’s retrieval began in the late 19th century AD/CE. Iconic Egyptian bas-reliefs and graphic hieroglyphic and cuneiform texts portray the proximate cause of the collapse as the invasions of the “Peoples-of-the-Sea” at the Nile Delta, the Turkish coast, and down into the heartlands of Syria and Palestine where armies clashed, famine-ravaged cities abandoned, and countrysides depopulated. Here we report palaeoclimate data from Cyprus for the Late Bronze Age crisis, alongside a radiocarbon-based chronology integrating both archaeological and palaeoclimate proxies, which reveal the effects of abrupt climate change-driven famine and causal linkage with the Sea People invasions in Cyprus and Syria. The statistical analysis of proximate and ultimate features of the sequential collapse reveals the relationships of climate-driven famine, sea-borne-invasion, region-wide warfare, and politico-economic collapse, in whose wake new societies and new ideologies were created.

Modern humans replaced Neandertals ∼40,000 y ago. Close to the time of replacement, Neandertals show behaviors similar to those of the modern humans arriving into Europe, including the use of specialized bone tools, body ornaments, and small blades. It is highly debated whether these modern behaviors developed before or as a result of contact with modern humans. Here we report the identification of a type of specialized bone tool, lissoir, previously only associated with modern humans. The microwear preserved on one of these lissoir is consistent with the use of lissoir in modern times to obtain supple, lustrous, and more impermeable hides. These tools are from a Neandertal context proceeding the replacement period and are the oldest specialized bone tools in Europe. As such, they are either a demonstration of independent invention by Neandertals or an indication that modern humans started influencing European Neandertals much earlier than previously believed. Because these finds clearly predate the oldest known age for the use of similar objects in Europe by anatomically modern humans, they could also be evidence for cultural diffusion from Neandertals to modern humans.

August 12, 2013

I had referred to this collection of papers before, and now all the PDFs appear to be available free of charge.

This seems fairly interesting:

Language and archeology: some methodological problems.1. Indo-European and Altaic landscapes

Anna Dybo

The article is the first part of a larger work that represents an attempt to systematize ourideas on the natural environment and material culture of the Proto-Indo-Europeans. It isbased on a more or less complete selection of reconstructed words from the appropriate semantic areas and on their comparison with a similar selection performed for a protolanguage of similar time depth, whose speakers evidently inhabited a territory that was notin contact with the Proto-Indo-European one — Proto-Altaic. In this part, only the words thatbelong to the semantic field of landscape terms are analyzed. The main conclusion is that thehypothesis of a steppe environment is more applicable for the Proto-Altaic population,whereas for Proto-Indo-Europeans a mountainous region seems more appropriate. As forthe water bodies, for Proto-Indo-Europeans we should suppose the existence of a sea (or of avery big lake), and for speakers of Proto-Altaic, the existence of very big rivers with seasonfloods

Mallory's article is also interesting as the latest public take on the PIE origins issue by the prominent champion of the Pontic-Caspian steppe hypothesis. It also alerted me to a study in Russian on the problem of Tocharian origins by Leonid Sverchkov. Sadly, I don't read Russian, but Mallory has a nice review of it in the Journal of Indo-European Studies, from which comes the following excerpt:

The second section of the book investigates CentralAsia as a cultural historical region. It briefly summarizes themajor Palaeolithic influences, then provides more detailabout the Mesolithic cultures of the region before settlingdown to a much more thorough description of theNeolithic cultures, among which much time is devoted tothe Kelteminar culture that occupied a broad area ofCentral Asia and which many earlier authors saw as criticalin explaining the origins of many of the neighboringcultures, among which would be included the Afanasievoculture of the Altay and Minusinsk Basin. The authorcontinues laying out the cultural-historical development ofCentral Asia up to the early Middle Ages.The third part is titled ‘Tokharians and the IndoEuropean problem” and the archaeological evidence seenearlier is then recast to provide arguments for a CentralAsian homeland for the Indo-Europeans. One of theperennial problems with searching out the origins of anyparticular Indo-European group is that all too oftenproponents of a particular theory provide an isolated‘solution’ divorced from the fact that it is only part of alarger puzzle and its pieces must make joins with the restof the Indo-European world. I have termed this the ‘totaldistribution principle’ and it is one of the tests of howserious we should deal with any partial solution to IndoEuropean expansions. In attempting to meet thisprinciple, one can hardly criticize the author as his finalsection is essentially a very detailed proposal for a ‘new’Indo-European homeland in Central Asia. Geographicallysituated not far from the earlier proposals of Gamkrelidzeand Ivanov, it does provide some legs to their generalpositioning of the Indo-European homeland but in a novelfashion. Sverchkov’s solution also embraces a series ofearlier suggestions or models but is truly his own in termsof its implementation.Sverchkov’s solution is fundamentally a rejection ofthose who would normally dismiss Central Asia as merely atransition zone across which migrating populations passedthrough.During the transition between the Mesolithicand Neolithic we find a vast Keltiminar culture occupyingthe entire region from the Urals and Caspian east to theAltay, and north of the Kopetdagh and northernAfghanistan. This region matches at least in areal extentthe type of homelands anchored in Europe such as thosewho have sought the Urheimat in the area of theLinearbandkeramik. To these Sverchkov also includes thesouthern agricultural regions of Jarmo and later Jeitunwhich would appear to lie outside the area normallyascribed to other non-Indo-European languages (Semitic,Elamite, Dravidian, Altaic, Uralic). This entire region thenfunctions as a broad Indo-European homeland. He suggeststhat the westward movement of the Halaf culture accountsfor the separation of the Anatolian branch. The ProtoTocharians begin within the Jeitun region and movedeastwards to arrive in Ferghana by the Bronze Age. Thearchaeological discussion emphasizes the presence ofpainted wares in both the Tarim Basin, especially in theregion where we find Tocharian B, and Ferghana, andthese persistent contacts are seen as indicating the spreadof the Tokharian languages. This pattern of Central Asiancontacts is seen even in the earliest cemeteries of theregion (Xiaohe, Gumagou) which, although lackingceramics altogether, possessed abundant evidence for bagshaped baskets which have been compared to the shapeand decorations of Kelteminar vessels. It might be notedthat precisely the same pot-to-basket argument has beenemployed by those who support a connection between theTarim Basin and the steppelands.The other Indo-European languages are accountedfor by very early (Neolithic) movements from Central Asiainto the Pontic-Caspian region. The Ayderbol culture ofKazakhstan, for example, is proposed as underlying theformation of the Dnieper-Donets culture of the Ukraineand as seen as the initial wave (roughly in the sense ofMarija Gimbutas) of the Italo-Celtic-Illyrians. The Neolithicand Eneolithic developments of the Volga-Ural region areunder the Kelteminar aegis and yield the later GermanicBalto-Slavic branches. Out of the steppe cultures (SrednyStog and Khvalynsk) and the neighboring Maykop culturehe derives the Yamnaya which in the guise of theAndronovo culture sets off the Aryanization of southernCentral Asia. Throughout this archaeological discussion theauthor relates his theories to a variety of linguisticproposals, e.g., Henning’s famous argument tying thenames of cultures on the frontiers of Mesopotamia withthose of the Tarim Basin

The European LD curve is steeper than either of the equilibrium curves in Fig. 10, suggesting a history of population expansion. This might re- ﬂect the spread of modern humans into Europe, the spread of farmers during the Neolithic, or the spread of Indo-European speakers. I evaluate these alternatives in a separate publication

arXiv:1308.1984 [q-bio.PE]

How Population Growth Affects Linkage Disequilibrium

Alan R. Rogers

Linkage disequilibrium (LD) is often summarized using the "LD curve," which relates the LD between pairs of sites to the distance that separates them along the chromosome. This paper shows how the LD curve responds to changes in population size. An expansion of population size generates an LD curve that declines steeply, especially if that expansion has followed a bottleneck. A reduction in size generates an LD curve that is high but relatively flat. In European data, the curve is steep, suggesting a history of population expansion. These conclusions emerge from the study of $\sigma_d^2$, a measure of LD that has never played a central role. It has been seen merely as an approximation to another measure, $r^2$. Yet $\sigma_d^2$ has different dynamical behavior and provides deeper time depth. Furthermore, it is easily estimated from data and can be predicted from population history using a fast, deterministic algorithm.

Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups – a profile which is very similar to the two other eastern European populations – Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively.

The first part of this research published previously proved without doubt that the metals dated to the Nordic Bronze Age found in Sweden were not smelted from the local copper ores. In this second part we present a detailed interpretation of these analytical data with the aim to identify the ore sources from which these metals originated. The interpretation of lead isotope and chemical data of 71 Swedish Bronze Age metals is based on the direct comparisons between the lead isotope data and geochemistry of ore deposits that are known to have produced copper in the Bronze Age. The presented interpretations of chemical and lead isotope analyses of Swedish metals dated to the Nordic Bronze Age are surprising and bring some information not known from previous work. Apart from a steady supply of copper from the Alpine ores in the North Tyrol, the main sources of copper seem to be ores from the Iberian Peninsula and Sardinia. Thus from the results presented here a new complex picture emerges of possible connectivities and flows in the Bronze Age between Scandinavia and Europe .

August 08, 2013

A new paper on the topic of Indian population history has just appeared in the American Journal of Human Genetics. In previous work it was determined that Indians trace their ancestry to two major groups, Ancestral North Indians (ANI) (= West Eurasians of some kind), and Ancestral South Indians (ASI) (= distant relatives of Andaman Islanders, existing today only in admixed form). The new paper demonstrates that admixture between these two groups took place ~4.2-1.9 thousand years ago.

The authors caution about this evidence of admixture:

It is also important to emphasize what our study has not shown. Although we have documented evidence for mixture in India between about 1,900 and 4,200 years BP, this does not imply migration from West Eurasia into India during this time. On the contrary, a recent study that searched for West Eurasian groups most closely related to the ANI ancestors of Indians failed to find any evidence for shared ancestry between the ANI and groups in West Eurasia within the past 12,500 years3 (although it is possible that with further sampling and new methods such relatedness might be detected). An alternative possibility that is also consistent with our data is that the ANI and ASI were both living in or near South Asia for a substantial period prior to their mixture. Such a pattern has been documented elsewhere; for example, ancient DNA studies of northern Europeans have shown that Neolithic farmers originating in Western Asia migrated to Europe about 7,500 years BP but did not mix with local hunter gatherers until thousands of years later to form the present-day populations of northern Europe.15, 16, 44 and 45

This is of course true, because admixture postdates migration and it is conceivable that the West Eurasian groups might not have admixed with ASI populations immediately after their arrival into South Asia. On the other hand, a long period of co-existence without admixture would be against much of human history (e.g., the reverse movement of the Roma into Europe, who picked up European admixture despite strong social pressure against it by both European and Roma communities, or the absorption of most Native Americans by incoming European, and later African, populations in post-Columbian times). It is difficult to imagine really long reproductive isolation between neighboring peoples.

Such reproductive isolation would require a cultural shift from a long period of endogamy (ANI migration, followed by ANI/ASI co-existence without admixture) to exogamy ~4.2-1.9kya (to explain the thoroughness of blending that left no group untouched), and then back to fairly strict exogamy (within the modern caste system). It might be simpler to postulate only one cultural shift (migration with admixture soon thereafter, with later introduction of endogamy which greatly diminished the admixture.

The authors cite the evidence from neolithic Sweden which does, indeed, suggest that the neolithic farmers this far north were "southern European" genetically and had not (yet) mixed with contemporary hunter-gatherers, as they must have done eventually. But, perhaps farmers and hunters could avoid each other during first contact, when Europe was sparsely populated. It is not clear whether the same could be said for India ~4 thousand years ago with the Indus Valley Civilization providing evidence for a large indigenous population that any intrusive group would have encountered. In any case, the problem of when the West Eurasian element arrived in India will probably be solved by relating it to events elsewhere in Eurasia, and, in particular, to the ultimate source of the "Ancestral North Indians".

It is also possible that some of the ANI-ASI admixture might actually pre-date migration. At present it's anyone's guess where the original limes between the west Eurasian and ASI worlds were. There is some mtDNA haplogroup M in Iran and Central Asia, which is otherwise rare in west Eurasia, so it is not inconceivable that ASI may have once extended outside the Indian subcontinent: the fact that it is concentrated today in southern India (hence its name) may indicate only the area of this element's maximum survival, rather than the extent of its original distribution. In any case, all mixture must have taken place somewhere in the vicinity of India.

A second interesting finding of the paper is that admixture dates in Indo-European groups are later than in Dravidian groups. This is demonstrated quite clearly in the rolloff figure on the left.Moreover, it does not seem that the admixture times for Indo-Europeans coincide with the appearance of the Indo-Aryans, presumably during the 2nd millennium BC: they are much later. I believe that this is fairly convincing evidence that north India has been affected by subsequent population movements from central Asia of "Indo-Scythian"-related populations, for which there is ample historical evidence. So, the difference in dates might be explained by secondary (later) admixture with other West Eurasians after the arrival of Indo-Aryans. Interestingly, the paper does not reject simple ANI-ASI admixture "often from tribal and traditionally lower-caste groups," while finding evidence for multiple layers of ANI ancestry in several other populations.

The authors also report that "we find that Georgians along with other Caucasus groups are consistent with sharing the most genetic drift with ANI". I had made a post on the differential relationship of ANI to Caucasus populations which seems to agree with this, and, of course, in various ADMIXTURE analyses, the component which I've labeled "West Asian" tends to be the major west Eurasian element in south Asia.

Here are the estimated admixture proportions/times from the paper:

Sadly, the warm and moist climate of India, and the adoption of cremation have probably destroyed any hope of studying much of its recent history with ancient DNA. On the other hand, the caste system has probably "fossilized" old socio-linguistic groups, allowing us to tell much by studying their differences and correlating them with groups outside India.

Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.

That next step happened slowly, and it seems to have required the spread of lactase persistence. The LP allele did not become common in the population until some time after it first emerged: Burger has looked for the mutation in samples of ancient human DNA and has found it only as far back as 6,500 years ago in northern Germany.

...

Some of the LeCHE participants are now probing further back in time, as part of a project named BEAN (Bridging the European and Anatolian Neolithic), which is looking at how the first farmers and herders made their way into Europe. Burger, Thomas and their BEAN collaborators will be in Turkey this summer, tracing the origins of the Neolithic using computer models and ancient-DNA analysis in the hope of better understanding who the early farmers were, and when they arrived in Europe.

August 02, 2013

A couple of important new papers on human Y-chromosome phylogeny appeared in Science today.

Francalacci et al. reconstructs the phylogeny of European Y-chromosomes based on a huge sample of 1,200 Sardinians. Naturally, Sardinians don't have every haplogroup in Europe or the planet, but with such a huge sample it was possible to find almost everything, minus obvious newcomers such as Uralic haplogroup N.

Poznik et al. build a human Y-chromosome phylogeny from 69 male genomes. The main thrust of their paper is to reconcile the "younger" Y-chromosome vs. "older" mtDNA in humans. In my opinion, that ship has sailed with the discovery of Y-haplogroup A00 which now makes the Y-chromosome MRCA of humans ("Adam") much older than the mtDNA one ("Eve").

And, indeed, the fact that the two are of different ages is not particularly troubling or in need of remedy, since for most reasonable models of human origins we do not expect them to be of the same age. Well, unless you believe the latest archaeological models that have early proto-sapiens perfecting their craft by scratching lines and perforating beads in some south African cave before spreading out to colonize the planet in one swift swoop.

The issue of the "discrepancy" aside, Poznik et al. resolve the issue of the binary structure of Y-haplogroup F, by showing that Y-haplogroup G (which is the Iceman's haplogroup, and the lineage most strongly associated with easly European farmers) branches off first from the tree.

Haplogroup G is an unambiguously west Eurasian lineage, so the fact that it is basal within F surely has implications about the origins of this most successful Eurasian group. The pattern is not quite clear, however, because the next most basal branch is H, which is unambiguously South Asian, and the next one after that is IJ vs. K, with IJ again being west Eurasian, with most east Eurasians nested within K. But, if we go up the tree, we see the split of C (Asian) vs. F (Eurasian), and further up DE (African+Eurasian) vs. CF (Eurasian). It seems to me that apart from the unambiguous African rooting of the entire tree, the rest of the topology paints a picture of a complex peopling of Eurasia, rather than a simple model of successive founder effects.

Another interesting finding of Poznik et al. is the discover of deep substructure within Y-haplogroup A-L419 (bottom of the picture).

The authors arrive at the following mutation rate:

Using entry to the Americas as a calibration point, we estimate a mutation rate of 0.82 × 10−9 per base pair (bp) per year [95% confidence interval (CI): 0.72 × 10−9 to 0.92 × 10−9/bp/year] (table S3).

This is notable for being lower than the directly estimated mutation rate of 1x10-9 of Xue et al. (2009).

The usefulness of "archaeological calibration" eludes me, which brings us back to Francalacci et al. who also archaeologically calibrate their mutation rate and find:

Considering that our analysis focused on approximately 8.97 Mbp of sequence from the Y chromosome X-degenerated region, this rate is equivalent to 0.53 × 10−9 bp−1 year−1.

So, the Francalacci et al. mutation rate is about half that of Xue et al., with that of Poznik et al. being intermediate. The Francalacci et al. rate was calibrated by "the initial expansion of the Sardinian population". Now, whether the current Sardinian population is descended from that initial expansion or from a later successful founder remains to be seen. In any case, using their ultra-slow mutation rate, these authors suggest that:

The main non-African super-haplogroup F-R shows an average variation of 534.8 (±28.7) SNPs, corresponding to a MRCA of ~110,000 years ago, in agreement with fossil remains of archaic Homo sapiens out of Africa (7, 18) though not with mtDNA, whose M and N super-haplogroups coalesce at a younger age (13). The main European subclades show a differentiation predating the peopling of Sardinia, with an average variation ranging from 70 to 120 SNPs (Table 1), corresponding to a coalescent age between 14,000 and 24,000 years ago, which is compatible with the postglacial peopling of Europe.

I am personally skeptical of all such archaeological calibrations and I'd like to see the mutation rate directly estimated using a well-behaved process (say, a 1,000-year old deep pedigree between two modern males separated by 60 meioses). It seems that there is no escape from mutation rate controversies in human genetics.

The most striking piece of data from this paper is the following figure:

Going from left-to-right:

R2 in Sardinia! This is extremely rare in Europe and underscores the importance of large sample sizes. It'd be wonderful to study it in the future in the context of, say, South Asian R2 which is much more numerous.

The clear "explosive" expansion of R1b-related lineages

A very deep common ancestry of haplogroups L and T.

Quite deep coalescences within Y-haplogroup J

"Explosive" growth of I2a1a1; this "southwest European" lineage attains its maximum in Sardinia and looks like a clear founder effect. It should definitely be visible in the ancient DNA record of the island.

Fairly deep splits within G2a. It would be interesting to see how G2 compares with Caucasian G1. We now know that G is very old lineage in West Eurasia (being the first split in haplogroup F), but how much of its present-diversity dates back to splits shortly after the haplogroup's appearance?

Finally, the deep splits within African haplogroup E correspond to the likely varied origins of these lineages

There's probably much more of interest in these twin papers, so if you notice anything in the supplementary materials, feel free to leave a comment.

Science 2 August 2013:
Vol. 341 no. 6145 pp. 562-565

DOI: 10.1126/science.1237619

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

G. David Poznik et al.

The Y chromosome and the mitochondrial genome have been used to estimate when the common patrilineal and matrilineal ancestors of humans lived. We sequenced the genomes of 69 males from nine populations, including two in which we find basal branches of the Y-chromosome tree. We identify ancient phylogenetic structure within African haplogroups and resolve a long-standing ambiguity deep within the tree. Applying equivalent methodologies to the Y chromosome and the mitochondrial genome, we estimate the time to the most recent common ancestor (TMRCA) of the Y chromosome to be 120 to 156 thousand years and the mitochondrial genome TMRCA to be 99 to 148 thousand years. Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages.

Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNA–based estimates.

August 01, 2013

A new paper was posted on the arXiv.
UPDATE (Feb 18, 2014): This has now been published in Genetics.

arXiv:1307.8263 [q-bio.PE]

Maximum likelihood evidence for Neandertal admixture in Eurasian populations from three genomes

Konrad Lohse, Laurent A.F. Frantz

Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population. The lack of a formal test to distinguish these scenarios has sparked recent controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. We derive the probability of mutational configurations in non-recombining sequence blocks under alternative histories of divergence with admixture and ancestral structure. Dividing the genome into short blocks makes it possible to compute maximum likelihood estimates of parameters under both models. We apply this method to triplets of human Neandertal genomes and quantify the relative support for models of long-term population structure in the ancestral African popuation and admixture from Neandertals into Eurasian populations after their expansion out of Africa. Our analysis allows us -- for the first time -- to formally reject a history of ancestral population structure and instead reveals strong support for admixture from Neandertals into Eurasian populations at a higher rate (3.4%-7.9%) than suggested previously.

There have been a few papers on the topic of Etruscan origins that argue in favor or against the Anatolian origin hypothesis. Two main lines of evidence exist on the topic: discontinuity between Etruscans and modern Tuscans (except some isolates); (perceived) similarity between Etrsucans' mtDNA and that of modern-day Turks.

Personally, I am not convinced either way, because I don't find it likely that a sample of modern-day Turks has much to tell us about the prehistoric relatives of the Etruscans. After all, modern-day Turks are descended from a a few dozen ancient Anatolian ethne plus a few extra-Anatolian influences from both west and east (and perhaps north and south) plus Central Asian Turkic influence minus Christian populations. We see evidence of genetic discontinuity in places with much simpler histories than Anatolia, so to claim that modern Turks have much of anything to tell us about Iron Age Etruscans is a not-so-believable proposition.

A similar complaint is that the specificity of the Etruscan gene pool can only be established by looking at their geographical neighbors. If Etruscans were intrusive to Italy, then, presumably, they would have retained differences from the surrounding Anatolian peoples.

A third (and perhaps more subtle) caveat is that "Etruscan" is polysemous. To the archaeologist and historian, it might mean a specific culture known from its remains and the texts of Romans and Greeks with which this culture interacted. To the linguist it might mean the language spoken by this culture when it attained literacy. To the geneticist it might mean the gene pool of individuals identified by archaeologists as "Etruscan".

These categories are not necessarily congruent. My favorite example is that of "Bulgarians" or "Croats", peoples who bear the name of a Turkic and Iranic people respectively, even though today they are geographically, culturally, and linguistically completely divorced from these antecedents. Or, the more controversial example of "Romans" themselves, whose nation spoke in historical times Latin, but whose histories preserved a memory of diverse origins, including, critically, an Anatolian genealogy for their eponymous ancestor.

So, the tale of Herodotus might be true (or false) on different levels. It might turn out that Etruscans did, in fact, form an isle of ancient west Anatolian genetics in Italy. Or, it might turn out that -as in the case of the Bulgarians- both language and genes are mostly native Italian, but the founding of the Etruscan nation can still be attributed to an extraneous influence. Or, perhaps Herodotus was 100% wrong, and Tyrrhenus never sailed to Italy.

Of course, I don't expect ancient DNA from all over Italy and all over Anatolia to materialize overnight, so studies such as this do help us constrain the space of possible solutions to the problem, i.e., a model with (i) substantial female participation in Etruscan colonization, (ii) genetic continuity in Anatolia to present-day Turks, and (iii) substantial contribution of Anatolian colonists to Etruscan gene pool may be falsified. But, assumptions (i-iii) describe only a small part of the space of models consistent with the Herodotean narrative.

Am J Phys Anthropol DOI: 10.1002/ajpa.22319

Genetic evidence does not support an etruscan origin in Anatolia

Francesca Tassi et al.

The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period.

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